3UUD

Crystal structure of hERa-LBD (Y537S) in complex with estradiol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and mechanistic insights into bisphenols action provide guidelines for risk assessment and discovery of bisphenol A substitutes.

Delfosse, V.Grimaldi, M.Pons, J.L.Boulahtouf, A.le Maire, A.Cavailles, V.Labesse, G.Bourguet, W.Balaguer, P.

(2012) Proc Natl Acad Sci U S A 109: 14930-14935

  • DOI: 10.1073/pnas.1203574109
  • Primary Citation of Related Structures:  
    3UUC, 3UUD, 3UUA, 3UU7

  • PubMed Abstract: 
  • Bisphenol A (BPA) is an industrial compound and a well known endocrine-disrupting chemical with estrogenic activity. The widespread exposure of individuals to BPA is suspected to affect a variety of physiological functions, including reproduction, development, and metabolism ...

    Bisphenol A (BPA) is an industrial compound and a well known endocrine-disrupting chemical with estrogenic activity. The widespread exposure of individuals to BPA is suspected to affect a variety of physiological functions, including reproduction, development, and metabolism. Here we report that the mechanisms by which BPA and two congeners, bisphenol AF and bisphenol C (BPC), bind to and activate estrogen receptors (ER) α and β differ from that used by 17β-estradiol. We show that bisphenols act as partial agonists of ERs by activating the N-terminal activation function 1 regardless of their effect on the C-terminal activation function 2, which ranges from weak agonism (with BPA) to antagonism (with BPC). Crystallographic analysis of the interaction between bisphenols and ERs reveals two discrete binding modes, reflecting the different activities of compounds on ERs. BPA and 17β-estradiol bind to ERs in a similar fashion, whereas, with a phenol ring pointing toward the activation helix H12, the orientation of BPC accounts for the marked antagonist character of this compound. Based on structural data, we developed a protocol for in silico evaluation of the interaction between bisphenols and ERs or other members of the nuclear hormone receptor family, such as estrogen-related receptor γ and androgen receptor, which are two known main targets of bisphenols. Overall, this study provides a wealth of tools and information that could be used for the development of BPA substitutes devoid of nuclear hormone receptor-mediated activity and more generally for environmental risk assessment.


    Organizational Affiliation

    Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale U1054, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 5048, Université Montpellier 1, 34090 Montpellier, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorA251Homo sapiensMutation(s): 1 
Gene Names: ESR1ESRNR3A1
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS:  P03372
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptorB251Homo sapiensMutation(s): 1 
Gene Names: ESR1ESRNR3A1
Find proteins for P03372 (Homo sapiens)
Explore P03372 
Go to UniProtKB:  P03372
NIH Common Fund Data Resources
PHAROS:  P03372
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 1C, D13Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EST
Query on EST

Download Ideal Coordinates CCD File 
E [auth A], G [auth B]ESTRADIOL
C18 H24 O2
VOXZDWNPVJITMN-ZBRFXRBCSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A], H [auth B], I [auth B]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

Download Ideal Coordinates CCD File 
J [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CSO
Query on CSO
AL-PEPTIDE LINKINGC3 H7 N O3 SCYS
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
ESTKi:  0.30000001192092896   nM  BindingDB
ESTIC50:  0.009999999776482582   nM  BindingDB
ESTIC50:  1.899999976158142   nM  BindingDB
ESTEC50:  0.029999999329447746   nM  BindingDB
ESTEC50:  0.20000000298023224   nM  BindingDB
ESTIC50:  1.399999976158142   nM  BindingDB
ESTEC50:  5.699999809265137   nM  BindingDB
ESTEC50:  0.5600000023841858   nM  BindingDB
ESTIC50:  0.3499999940395355   nM  BindingDB
ESTIC50:  0.10999999940395355   nM  BindingDB
ESTEC50:  10   nM  BindingDB
ESTEC50:  5.699999809265137   nM  BindingDB
ESTKi:  0.18000000715255737   nM  BindingDB
ESTIC50:  1.7000000476837158   nM  BindingDB
ESTIC50:  0.699999988079071   nM  BindingDB
ESTIC50:  1.2000000476837158   nM  BindingDB
ESTEC50:  2.200000047683716   nM  BindingDB
ESTEC50:  2.7699999809265137   nM  BindingDB
ESTIC50:  3.4000000953674316   nM  BindingDB
ESTIC50:  4.400000095367432   nM  BindingDB
ESTEC50:  0.11999999731779099   nM  BindingDB
ESTIC50:  5.900000095367432   nM  BindingDB
ESTIC50:  2.200000047683716   nM  BindingDB
ESTEC50:  1.100000023841858   nM  BindingDB
ESTEC50:  3   nM  BindingDB
ESTKi:  0.11999999731779099   nM  BindingDB
ESTIC50:  0.75   nM  BindingDB
ESTEC50:  0   nM  BindingDB
ESTEC50:  0.09000000357627869   nM  BindingDB
ESTIC50:  0.5   nM  BindingDB
ESTEC50:  0.15000000596046448   nM  BindingDB
ESTEC50:  1   nM  BindingDB
ESTEC50:  3.200000047683716   nM  BindingDB
ESTKi:  0.20999999344348907   nM  BindingDB
ESTEC50:  0.25999999046325684   nM  BindingDB
ESTKi:  100   nM  BindingDB
ESTEC50:  0.75   nM  BindingDB
ESTKi:  0.8299999833106995   nM  BindingDB
ESTIC50:  4.699999809265137   nM  BindingDB
ESTEC50:  1.0499999523162842   nM  BindingDB
ESTIC50:  3   nM  BindingDB
ESTIC50:  3.5999999046325684   nM  BindingDB
ESTKd:  3   nM  BindingDB
ESTIC50:  2   nM  BindingDB
ESTIC50:  1.7999999523162842   nM  BindingDB
ESTIC50:  5.699999809265137   nM  BindingDB
ESTKi:  0.14000000059604645   nM  BindingDB
ESTIC50:  1.5   nM  BindingDB
ESTIC50:  1   nM  BindingDB
ESTIC50:  11   nM  BindingDB
ESTEC50:  0.3700000047683716   nM  BindingDB
ESTIC50:  0.8999999761581421   nM  BindingDB
ESTIC50:  12.5   nM  BindingDB
ESTEC50:  0.10999999940395355   nM  BindingDB
ESTEC50:  0.3100000023841858   nM  BindingDB
ESTIC50:  1.2999999523162842   nM  BindingDB
ESTKi:  12   nM  BindingDB
ESTIC50:  10   nM  BindingDB
ESTEC50:  2.4000000953674316   nM  BindingDB
ESTEC50:  0.019999999552965164   nM  BindingDB
ESTIC50:  2   nM  BindingDB
ESTKd:  100   nM  BindingDB
ESTIC50:  4   nM  BindingDB
ESTIC50:  46   nM  BindingDB
ESTEC50:  0.1599999964237213   nM  BindingDB
ESTEC50:  3.799999952316284   nM  BindingDB
ESTIC50:  24   nM  BindingDB
ESTEC50:  0.07999999821186066   nM  BindingDB
ESTIC50:  0.44999998807907104   nM  BindingDB
ESTKi:  2   nM  BindingDB
ESTIC50:  28   nM  BindingDB
ESTEC50:  0.18000000715255737   nM  BindingDB
ESTEC50:  0.49000000953674316   nM  BindingDB
ESTIC50:  18   nM  BindingDB
ESTEC50:  0.699999988079071   nM  BindingDB
ESTKd:  0.20000000298023224   nM  BindingDB
ESTIC50:  0.4099999964237213   nM  BindingDB
ESTKi:  0.1599999964237213   nM  BindingDB
ESTIC50:  3.200000047683716   nM  BindingDB
ESTIC50:  4.800000190734863   nM  BindingDB
ESTEC50:  0.28999999165534973   nM  BindingDB
ESTIC50:  0.8199999928474426   nM  BindingDB
ESTEC50:  0.47999998927116394   nM  BindingDB
ESTIC50:  1.350000023841858   nM  BindingDB
ESTKi:  2.200000047683716   nM  BindingDB
ESTIC50:  0.5699999928474426   nM  BindingDB
ESTIC50:  1.600000023841858   nM  BindingDB
ESTEC50:  2.299999952316284   nM  BindingDB
ESTEC50:  0.5899999737739563   nM  BindingDB
ESTEC50:  0.009999999776482582   nM  BindingDB
ESTEC50:  0.10000000149011612   nM  BindingDB
ESTKi:  0.10999999940395355   nM  BindingDB
ESTEC50:  0.07000000029802322   nM  BindingDB
ESTKi:  0.6499999761581421   nM  BindingDB
ESTIC50:  1.899999976158142   nM  BindingDB
ESTEC50:  0.05000000074505806   nM  BindingDB
ESTIC50:  21.040000915527344   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.23α = 90
b = 82.01β = 111.06
c = 58.93γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHENIXmodel building
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release
  • Version 1.1: 2012-09-26
    Changes: Database references